Methods of synthesizing heteromultimeric polypeptides in yeast using a haploid mating strategy

ABSTRACT

Methods are provided for the synthesis and secretion of recombinant hetero-multimeric proteins in mating competent yeast. A first expression vector is transformed into a first haploid cell; and a second expression vector is transformed into a second haploid cell. The transformed haploid cells, each individually synthesizing a non-identical polypeptide, are identified and then genetically crossed or fused. The resulting diploid strains are utilized to produce and secrete fully assembled and biologically functional hetero-multimeric protein.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.14/853,292, which was filed Sep. 14, 2015, now U.S. Pat. No. 10,259,883,which is a Divisional of U.S. patent application Ser. No. 14/165,896,filed Jan. 28, 2014, now U.S. Pat. No. 10,155,819, which is a divisionalof U.S. patent application Ser. No. 13/598,885, filed Aug. 30, 2012, nowU.S. Pat. No. 8,709,756, which is a divisional of U.S. patentapplication Ser. No. 10/577,074, filed May 7, 2007, now U.S. Pat. No.8,268,582, which is a U.S. 371 National Stage Appl. Of Int'l Appl. No.PCT/US2004/035302 filed Oct. 22, 2004, which claims priority to U.S.Provisional Appl. No. 60/513,876 filed Oct. 22, 2003.

The disclosures of each and all of the aforementioned applications isincorporated herein by reference in their entireties.

SEQUENCE LISTING

The sequence listing in the file named “43257o1208.txt” having a size of13,188 bytes that was created Mar. 11, 2019 is hereby incorporated byreference in its entirety.

BACKGROUND OF THE INVENTION

Recombinant protein production is an essential activity for highthroughput screening, functional validation, structural biology, andproduction of pharmaceutical polypeptides. Escherichia coli is a widelyused organism for the expression of heterologous proteins because iteasily grows to a high cell density on inexpensive substrates, and haswell-established genetic techniques and expression vectors. However,this is not always sufficient for the efficient production of activebiomolecules. In order to be biologically active, polypeptide chainshave to fold into the correct native three-dimensional structure,including the appropriate formation of disulfide bonds, and may furtherrequire correct association of multiple chains.

Although the active state of the protein may be thermodynamicallyfavored, the time-scale for folding can vary from milliseconds to days.Kinetic barriers are introduced, for example, by the need for alignmentof subunits and sub-domains. And particularly with eukaryotic proteins,covalent reactions must take place for the correctly folded protein toform. The latter types of reaction include disulfide bond formation,cis/trans isomerization of the polypeptide chain around proline peptidebonds, preprotein processing and the ligation of prosthetic groups.These kinetic limitations can result in the accumulation of partiallyfolded intermediates that contain exposed hydrophobic ‘sticky’ surfacesthat promote self-association and formation of aggregates.

Antibodies are tetrameric proteins, which have many uses in clinicaldiagnosis and therapy. Each antibody tetramer is composed of twoidentical light chains and two identical heavy chains. Pure human orhumanized antibodies of a specific type are difficult or impossible topurify in sufficient amounts for many purposes from natural sources. Asa consequence, biotechnology and pharmaceutical companies have turned torecombinant DNA-based methods to prepare them on a large scale. Theproduction of functional antibodies requires not just the synthesis ofthe two polypeptides but also a number of post-translationalmodifications, including proteolytic processing of the N-terminalsecretion signal sequence; proper folding and assembly of thepolypeptides into tetramers; formation of disulfide bonds; and specificN-linked glycosylation. All of these events take place in the eukaryoticcell secretory pathway, an organelle complex unique to eukaryotic cells.

Recombinant synthesis of such complex proteins has had to rely on highereukaryotic tissue culture-based systems for biologically activematerial. However, mammalian tissue culture based production systems aresignificantly more expensive and complicated than microbial fermentationmethods. In addition, there continues to be questions regardingtherapeutic products produced using materials derived from animalby-products.

As a eukaryote, Pichia pastoris has many of the advantages of highereukaryotic expression systems such as protein processing, proteinfolding, and posttranslational modification, while being as easy tomanipulate as E. coli or Saccharomyces cerevisiae. It is faster, easier,and less expensive to use than other eukaryotic expression systems suchas baculovirus or mammalian tissue culture, and generally gives higherexpression levels. As a yeast, it shares the advantages of molecular andgenetic manipulations with Saccharomyces. These features make Pichiavery useful as a protein expression system.

Many of the techniques developed for Saccharomyces may be applied toPichia. These include transformation by complementation; gene disruptionand gene replacement. In addition, the genetic nomenclature used forSaccharomyces has been applied to Pichia. There is alsocross-complementation between gene products in both Saccharomyces andPichia. Several wild-type genes from Saccharomyces complement comparablemutant genes in Pichia.

Heterologous expression in Pichia pastoris can be either intracellularor secreted. Secretion requires the presence of a signal sequence on theexpressed protein to target it to the secretory pathway. While severaldifferent secretion signal sequences have been used successfully,including the native secretion signal present on some heterologousproteins, success has been variable. A potential advantage to secretionof heterologous proteins is that Pichia pastoris secretes very lowlevels of native proteins. That, combined with the very low amount ofprotein in the minimal Pichia growth medium, means that the secretedheterologous protein comprises the vast majority of the total protein inthe medium and serves as the first step in purification of the protein.

Many species of yeast, including Pichia, are mating competent. Thisenables two distinct haploid strains to mate naturally and generate adiploid species possessing two chromosomal copies.

Although P. pastoris has been used successfully for the production ofvarious heterologous proteins, e.g., hepatitis B surface antigen (Gregget al. (1987) Bio/Technology 5:479), lysozyme and invertase (Digan etal. (1988) Dev. Indust. Micro. 29:59; Tschopp et al. (1987)Bio/Technology 5:1305), endeavors to produce other heterologous geneproducts in Pichia, especially by secretion, have given mixed results.At the present level of understanding of the P. pastoris expressionsystem, it is unpredictable whether a given gene can be expressed to anappreciable level in this yeast or whether Pichia will tolerate thepresence of the recombinant gene product in its cells. Further, it isespecially difficult to foresee if a particular protein will be secretedby P. pastoris, and if it is, at what efficiency.

The present invention provides improved methods for the secretion ofheterologous heteromultimers from mating competent yeast, includingPichia species.

SUMMARY OF INVENTION

Methods are provided for the synthesis and secretion of recombinanthetero-multimeric proteins in mating competent yeast. Hetero-multimericproteins of interest comprise at least two non-identical polypeptidechains, e.g. antibody heavy and light chains, MHC alpha and beta chains;and the like. An expression vector is provided for each non-identicalpolypeptide chain.

Each expression vector is transformed into a haploid yeast cell. In someembodiments of the invention, the haploid yeast cell is geneticallymarked, where the haploid yeast cell is one of a complementary pair. Afirst expression vector is transformed into one haploid cell and asecond expression vector is transformed into a second haploid cell.Where the haploid cells are to be mated this will be through directgenetic fusion, or a similar event is induced with spheroplast fusion.

The expression levels of the non-identical polypeptides in the haploidcells may be individually calibrated, and adjusted through appropriateselection, vector copy number, promoter strength and/or induction andthe like. In one embodiment of the invention, the promoter in eachexpression vector is different. In another embodiment of the invention,the same promoter is provided for each. Promoters may be constitutive orinducible.

The transformed haploid cells, each individually synthesizing anon-identical polypeptide, are identified and then genetically crossedor fused. The resulting diploid strains are utilized to produce andsecrete fully assembled and biologically functional hetero-multimericprotein. The diploid methodology allows optimized subunit pairing toenhance full-length product generation and secretion.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-1D. Generation of assembled full length recombinant antibody.Immunoblot detection methodology was used to characterize the parentalhaploid Pichia strains, each producing a subunit of the antibody andtarget diploid strain producing both subunits that form the fullyassembled antibody. The yeast strains shown in FIG. 1A show a staticculture of each of the representative strains, where the top portion isthe distinct haploids strains containing Heavy (H) and Light (L) chainsubunits respectively; the bottom the mated stable diploid producingboth subunits. FIG. 1B shows selective detection of the H chain, whichis found only in the parental H chain haploid, and mated diploidcontaining both H and L. FIG. 1C shows general detection of H & Lchains, which establishes that protein production is active in all threestrains. FIG. 1D shows selective detection in the diploid strain ofcorrectly assembled full antibody, confirming that only the diploidsystem is capable of generating fully assembled antibody.

FIG. 2. Full length antibody production in Pichia pastoris. Heterologousexpression of full-length antibody was conducted using a diploid Pichiapastoris strain. Exported antibody protein was isolated from conditionedmedia using Protein A affinity chromatography. An aliquot of the peakfraction is shown. The human IgG standard was derived from purifiedpooled human IgG.

FIG. 3. Assembled antibody was detected and characterized from mediasupernatants from subclones of diploid Pichia pastoris strains, whichwere engineered to produce full-length mouse/human chimeric antibody.Microtiter plates were coated with Anti-human Fc selective antibodies tocapture the antibody from the culture media. Correctly assembledantibody was detected through the use of a human selective (Fab′)2,which recognized the paired heavy CHI and K light chain constantregions. Serial dilutions of clarified media were applied to the plate.Development was through standard ELISA visualization methods. Thedetection is selective as shown by the lack of any detectable signal inthe mIgG standard.

FIG. 4. Pichia generated recombinant antibody stains CD3 containingJurkat T-cells as well as traditional mammalian-derived antibody. JurkatT-cells were immobilized on glass slides and staining was conductedusing the anti-CD3 antibody generated in yeast and mammalian cells.Detection was performed using a biotinylated-conjugated anti-rodentsecondary antibody, and developed with an HRP-streptavidin derivative.The imagines are representative field of slide treated with eachrecombinant antibody. Background is control for development andconducted in the absence of the primary anti-CD3 antibody.

DETAILED DESCRIPTION OF THE EMBODIMENTS

Recombinant hetero-multimeric proteins are secreted from diploid strainsof mating competent yeast. A pair of genetically marked yeast haploidcells are transformed with expression vectors comprising subunits of theheteromultimeric protein. One haploid cell comprises a first expressionvector, and a second haploid cell comprises a second expression vector.Optionally, additional expression vectors may be introduced into thehaploid or diploid cells; or the first or second expression vectors maycomprise additional coding sequences; for the synthesis ofheterotrimers; heterotetramers; etc. The expression levels of thenon-identical polypeptides may be individually calibrated, and adjustedthrough appropriate selection, vector copy number, promoter strengthand/or induction and the like. The transformed haploid cells aregenetically crossed or fused. The resulting diploid or tetraploidstrains are utilized to produce and secrete fully assembled andbiologically functional hetero-multimeric protein.

The use of diploid or tetraploid cells for protein production providesfor unexpected benefits. The cells can be grown for production purposes,i.e. scaled up, and for extended periods of time, in conditions that canbe deleterious to the growth of haploid cells, which conditions mayinclude high cell density; growth in minimal media; growth at lowtemperatures; stable growth in the absence of selective pressure; andwhich may provide for maintenance of heterologous gene sequenceintegrity and maintenance of high level expression over time. Thesebenefits may arise, at least in part, from the creation of diploidstrains from two distinct parental haploid strains. Such haploid strainscan comprise numerous minor autotrophic mutations, which mutations arecomplemented in the diploid or tetraploid, enabling growth under highlyselective conditions.

Definitions

It is to be understood that this invention is not limited to theparticular methodology, protocols, cell lines, animal species or genera,and reagents described, as such may vary. It is also to be understoodthat the terminology used herein is for the purpose of describingparticular embodiments only, and is not intended to limit the scope ofthe present invention which will be limited only by the appended claims.

As used herein the singular forms “a”, “and”, and “the” include pluralreferents unless the context clearly dictates otherwise. Thus, forexample, reference to “a cell” includes a plurality of such cells andreference to “the protein” includes reference to one or more proteinsand equivalents thereof known to those skilled in the art, and so forth.All technical and scientific terms used herein have the same meaning ascommonly understood to one of ordinary skill in the art to which thisinvention belongs unless clearly indicated otherwise.

Mating competent yeast species. Such species of yeast exist in a haploidand a diploid form. The diploid cells may, under appropriate conditions,proliferate for indefinite number of generations in the diploid form.Diploid cells can also sporulate to form haploid cells. In addition,sequential mating can result in tetraploid strains through furthermating of the auxotrophic diploids.

In one embodiment of the invention, the mating competent yeast is amember of the Saccharomycetaceae family, which includes the generaArxiozyma; Ascobotryozyma; Citeromyces; Debaryomyces; Dekkera;Eremothecium; Issatchenkia; Kazachstania; Kluyveromyces; Kodamaea;Lodderomyces; Pachysolen; Pichia; Saccharomyces; Saturnispora;Tetrapisispora; Torulaspora; Williopsis; and Zygosaccharomyces.

The genus Pichia is of particular interest. Pichia comprises a number ofspecies, including the species Pichia pastoris, Pichia methanolica, andHansenula polymorpha (Pichia angusta). Most preferred is the speciesPichia pastoris.

Haploid Yeast Cell: A cell having a single copy of each gene of itsnormal genomic (chromosomal) complement.

Diploid Yeast Cell: A cell having two copies (alleles) of every gene ofits normal genomic complement, typically formed by the process of fusion(mating) of two haploid cells.

Tetraploid Yeast Cell. A cell having four copies (alleles) of every geneof its normal genomic complement, typically formed by the process offusion (mating) of two haploid cells. Tetraploids may carry two, three,or four different cassettes. Such tetraploids might be obtained in S.cerevisiae by selective mating homozygotic heterothallic a/a andalpha/alpha diploids and in Pichia by sequential mating of haploids toobtain auxotrophic diploids. For example, a [met his] haploid can bemated with [ade his] haploid to obtain diploid [his]; and a [met arg]haploid can be mated with [ade arg] haploid to obtain diploid [arg];then the diploid [his]×diploid [arg] to obtain a tetraploid prototroph.It will be understood by those of skill in the art that reference to thebenefits and uses of diploid cells may also apply to tetraploid cells.

Yeast Mating: The process by which two haploid yeast cells naturallyfuse to form one diploid yeast cell.

Meiosis: The process by which a diploid yeast cell undergoes reductivedivision to form four haploid spore products. Each spore may thengerminate and form a haploid vegetatively growing cell line.

Selectable Marker: A selectable marker is a gene or gene fragment thatconfers a growth phenotype (physical growth characteristic) on a cellreceiving that gene as, for example through a transformation event. Theselectable marker allows that cell to survive and grow in a selectivegrowth medium under conditions in which cells that do not receive thatselectable marker gene cannot grow. Selectable marker genes generallyfall into several types, including positive selectable marker genes suchas a gene that confers on a cell resistance to an antibiotic or otherdrug, temperature when two ts mutants are crossed or a ts mutant istransformed; negative selectable marker genes such as a biosyntheticgene that confers on a cell the ability to grow in a medium without aspecific nutrient needed by all cells that do not have that biosyntheticgene, or a mutagenized biosynthetic gene that confers on a cellinability to grow by cells that do not have the wild type gene; and thelike. Suitable markers include but are not limited to: ZEO; G418; HIS 5;LYS3; MET1; MET3a; ADE1; ADE3; URA3; and the like.

Expression Vector: These DNA species contain elements that facilitatemanipulation for the expression of a foreign protein within the targethost cell. Conveniently, manipulation of sequences and production of DNAfor transformation is first performed in a bacterial host, e.g. E. coli,and usually vectors will include sequences to facilitate suchmanipulations, including a bacterial origin of replication andappropriate bacterial selection marker. Selectable markers encodeproteins necessary for the survival or growth of transformed host cellsgrown in a selective culture medium. Host cells not transformed with thevector containing the selection gene will not survive in the culturemedium. Typical selection genes encode proteins that (a) conferresistance to antibiotics or other toxins, (b) complement auxotrophicdeficiencies, or (c) supply critical nutrients not available fromcomplex media.

Expression vectors for use in the methods of the invention will furtherinclude yeast specific sequences, including a selectable auxotrophic ordrug marker for identifying transformed yeast strains. A drug marker mayfurther be used to amplify copy number of the vector in a yeast hostcell.

The polypeptide coding sequence of interest is operably linked totranscriptional and translational regulatory sequences that provide forexpression of the polypeptide in yeast cells. These vector componentsmay include, but are not limited to, one or more of the following: anenhancer element, a promoter, and a transcription termination sequence.Sequences for the secretion of the polypeptide may also be included,e.g. a signal sequence, and the like. A yeast origin of replication isoptional, as expression vectors are often integrated into the yeastgenome.

In one embodiment of the invention, the polypeptide of interest isoperably linked, or fused, to sequences providing for optimizedsecretion of the polypeptide from yeast diploid cells.

Nucleic acids are “operably linked” when placed into a functionalrelationship with another nucleic acid sequence. For example, DNA for asignal sequence is operably linked to DNA for a polypeptide if it isexpressed as a preprotein that participates in the secretion of thepolypeptide; a promoter or enhancer is operably linked to a codingsequence if it affects the transcription of the sequence. Generally,“operably linked” means that the DNA sequences being linked arecontiguous, and, in the case of a secretory leader, contiguous and inreading phase. However, enhancers do not have to be contiguous. Linkingis accomplished by ligation at convenient restriction sites oralternatively via a PCR/recombination method familiar to those skilledin the art (Gateway® Technology; Invitrogen, Carlsbad Calif.). If suchsites do not exist, the synthetic oligonucleotide adapters or linkersare used in accordance with conventional practice.

Promoters are untranslated sequences located upstream (5′) to the startcodon of a structural gene (generally within about 100 to 1000 bp) thatcontrol the transcription and translation of particular nucleic acidsequence to which they are operably linked. Such promoters fall intoseveral classes: inducible, constitutive, and repressible promoters thatincrease levels of transcription in response to absence of a repressor.Inducible promoters may initiate increased levels of transcription fromDNA under their control in response to some change in cultureconditions, e.g., the presence or absence of a nutrient or a change intemperature.

The yeast promoter fragment may also serve as the site for homologousrecombination and integration of the expression vector into the samesite in the yeast genome; alternatively a selectable marker is used asthe site for homologous recombination. Pichia transformation isdescribed in Cregg et al. (1985) Mol. Cell. Biol. 5:3376-3385.

Examples of suitable promoters from Pichia include the AOX1 and promoter(Cregg et al. (1989) Mol. Cell. Biol. 9:1316-1323); ICL1 promoter(Menendez et al. (2003) Yeast 20(13):1097-108);glyceraldehyde-3-phosphate dehydrogenase promoter (GAP) (Waterham et al.(1997) Gene 186(1):37-44); and FLD1 promoter (Shen et al. (1998) Gene216(1):93-102). The GAP promoter is a strong constitutive promoter andthe AOX and FLD1 promoters are inducible.

The polypeptides of interest may be produced recombinantly not onlydirectly, but also as a fusion polypeptide with a heterologouspolypeptide, e.g. a signal sequence or other polypeptide having aspecific cleavage site at the N-terminus of the mature protein orpolypeptide. In general, the signal sequence may be a component of thevector, or it may be a part of the polypeptide coding sequence that isinserted into the vector. The heterologous signal sequence selectedpreferably is one that is recognized and processed through one of thestandard pathways available within the host cell. The S. cerevisiaealpha factor pre-pro signal has proven effective in the secretion of avariety of recombinant proteins from P. pastoris. Secretion signals ofinterest also include mammalian signal sequences, which may beheterologous to the protein being secreted, or may be a native sequencefor the protein being secreted. Signal sequences include pre-peptidesequences, and in some instances may include propeptide sequences. Manysuch signal sequences are known in the art, including the signalsequences found on immunoglobulin chains, e.g. K28 preprotoxin sequence,PHA-E, FACE, human MCP-1, human serum albumin signal sequences, human Igheavy chain, human Ig light chain, and the like. For example, seeHashimoto et. al. Protein Eng 11(2) 75 (1998); and Kobayashi et. al.Therapeutic Apheresis 2(4) 257 (1998).

Transcription may be increased by inserting a transcriptional activatorsequence into the vector. These activators are cis-acting elements ofDNA, usually about from 10 to 300 bp, which act on a promoter toincrease its transcription. Transcriptional enhancers are relativelyorientation and position independent, having been found 5′ and 3′ to thetranscription unit, within an intron, as well as within the codingsequence itself. The enhancer may be spliced into the expression vectorat a position 5′ or 3′ to the coding sequence, but is preferably locatedat a site 5′ from the promoter.

Expression vectors used in eukaryotic host cells may also containsequences necessary for the termination of transcription and forstabilizing the mRNA. Such sequences are commonly available from 3′ tothe translation termination codon, in untranslated regions of eukaryoticor viral DNAs or cDNAs. These regions contain nucleotide segmentstranscribed as polyadenylated fragments in the untranslated portion ofthe mRNA.

Construction of suitable vectors containing one or more of theabove-listed components employs standard ligation techniques orPCR/recombination methods. Isolated plasmids or DNA fragments arecleaved, tailored, and re-ligated in the form desired to generate theplasmids required or via recombination methods. For analysis to confirmcorrect sequences in plasmids constructed, the ligation mixtures areused to transform host cells, and successful transformants selected byantibiotic resistance (e.g. ampicillin or Zeocin) where appropriate.Plasmids from the transformants are prepared, analyzed by restrictionendonuclease digestion and/or sequenced.

As an alternative to restriction and ligation of fragments,recombination methods based on att sites and recombination enzymes maybe used to insert DNA sequences into a vector. Such methods aredescribed, for example, by Landy (1989) Ann. Rev. Biochem. 58:913-949;and are known to those of skill in the art. Such methods utilizeintermolecular DNA recombination that is mediated by a mixture of lambdaand E. coli-encoded recombination proteins. Recombination occurs betweenspecific attachment (att) sites on the interacting DNA molecules. For adescription of att sites see Weisberg and Landy (1983) Site-SpecificRecombination in Phage Lambda, in Lambda I I, Weisberg, ed. (Cold SpringHarbor, N.Y.:Cold Spring Harbor Press), pp. 211-250. The DNA segmentsflanking the recombination sites are switched, such that afterrecombination, the att sites are hybrid sequences comprised of sequencesdonated by each parental vector. The recombination can occur betweenDNAs of any topology.

Att sites may be introduced into a sequence of interest by ligating thesequence of interest into an appropriate vector; generating a PCRproduct containing att B sites through the use of specific primers;generating a cDNA library cloned into an appropriate vector containingatt sites; and the like.

Folding, as used herein, refers to the three-dimensional structure ofpolypeptides and proteins, where interactions between amino acidresidues act to stabilize the structure. While non-covalent interactionsare important in determining structure, usually the proteins of interestwill have intra- and/or intermolecular covalent disulfide bonds formedby two cysteine residues. For naturally occurring proteins andpolypeptides or derivatives and variants thereof, the proper folding istypically the arrangement that results in optimal biological activity,and can conveniently be monitored by assays for activity, e.g. ligandbinding, enzymatic activity, etc.

In some instances, for example where the desired product is of syntheticorigin, assays based on biological activity will be less meaningful. Theproper folding of such molecules may be determined on the basis ofphysical properties, energetic considerations, modeling studies, and thelike.

The expression host may be further modified by the introduction ofsequences encoding one or more enzymes that enhance folding anddisulfide bond formation, i.e. foldases, chaperonins, etc. Suchsequences may be constitutively or inducibly expressed in the yeast hostcell, using vectors, markers, etc. as known in the art. Preferably thesequences, including transcriptional regulatory elements sufficient forthe desired pattern of expression, are stably integrated in the yeastgenome through a targeted methodology.

For example, the eukaryotic PDI is not only an efficient catalyst ofprotein cysteine oxidation and disulfide bond isomerization, but alsoexhibits chaperone activity. Co-expression of PDI can facilitate theproduction of active proteins having multiple disulfide bonds. Also ofinterest is the expression of BIP (immunoglobulin heavy chain bindingprotein); cyclophilin; and the like. In one embodiment of the invention,each of the haploid parental strains expresses a distinct foldingenzyme, e.g. one strain may express BIP, and the other strain mayexpress PDI.

The terms “desired protein” or “target protein” are used interchangeablyand refer generally to any secreted protein having 2 or morenon-identical polypeptide chains, where such chains are independentlysynthesized, i.e. not resulting from post-translational cleavage of asingle polypeptide chain. The polypeptides are heterologous, i.e.,foreign, to the yeast. Preferably, mammalian polypeptides, i.e.polypeptides encoded in a mammalian genome are used.

In a preferred embodiment, the protein is an antibody. The term“antibody” is intended to include any polypeptide chain-containingmolecular structure with a specific shape that fits to and recognizes anepitope, where one or more non-covalent binding interactions stabilizethe complex between the molecular structure and the epitope. Thearchetypal antibody molecule is the immunoglobulin, and all types ofimmunoglobulins, IgG, IgM, IgA, IgE, IgD, etc., from all sources, e.g.human, rodent, rabbit, cow, sheep, pig, dog, other mammals, chicken,other avians, etc., are considered to be “antibodies.” Numerous antibodycoding sequences have been described; and others may be raised bymethods well-known in the art.

For example, antibodies or antigen binding fragments may be produced bygenetic engineering. In this technique, as with other methods,antibody-producing cells are sensitized to the desired antigen orimmunogen. The messenger RNA isolated from antibody producing cells isused as a template to make cDNA using PCR amplification. A library ofvectors, each containing one heavy chain gene and one light chain generetaining the initial antigen specificity, is produced by insertion ofappropriate sections of the amplified immunoglobulin cDNA into theexpression vectors. A combinatorial library is constructed by combiningthe heavy chain gene library with the light chain gene library. Thisresults in a library of clones which co-express a heavy and light chain(resembling the Fab fragment or antigen binding fragment of an antibodymolecule). The vectors that carry these genes are co-transfected into ahost cell. When antibody gene synthesis is induced in the transfectedhost, the heavy and light chain proteins self-assemble to produce activeantibodies that can be detected by screening with the antigen orimmunogen.

Antibody coding sequences of interest include those encoded by nativesequences, as well as nucleic acids that, by virtue of the degeneracy ofthe genetic code, are not identical in sequence to the disclosed nucleicacids, and variants thereof. Variant polypeptides can include amino acid(aa) substitutions, additions or deletions. The amino acid substitutionscan be conservative amino acid substitutions or substitutions toeliminate non-essential amino acids, such as to alter a glycosylationsite, or to minimize misfolding by substitution or deletion of one ormore cysteine residues that are not necessary for function. Variants canbe designed so as to retain or have enhanced biological activity of aparticular region of the protein (e.g., a functional domain, catalyticamino acid residues, etc). Variants also include fragments of thepolypeptides disclosed herein, particularly biologically activefragments and/or fragments corresponding to functional domains.Techniques for in vitro mutagenesis of cloned genes are known. Alsoincluded in the subject invention are polypeptides that have beenmodified using ordinary molecular biological techniques so as to improvetheir resistance to proteolytic degradation or to optimize solubilityproperties or to render them more suitable as a therapeutic agent.

Chimeric antibodies may be made by recombinant means by combining thevariable light and heavy chain regions (VK and VH), obtained fromantibody producing cells of one species with the constant light andheavy chain regions from another. Typically chimeric antibodies utilizerodent or rabbit variable regions and human constant regions, in orderto produce an antibody with predominantly human domains. The productionof such chimeric antibodies is well known in the art, and may beachieved by standard means (as described, e.g., in U.S. Pat. No.5,624,659, incorporated fully herein by reference).

Humanized antibodies are engineered to contain even more human-likeimmunoglobulin domains, and incorporate only thecomplementarity-determining regions of the animal-derived antibody. Thisis accomplished by carefully examining the sequence of thehyper-variable loops of the variable regions of the monoclonal antibody,and fitting them to the structure of the human antibody chains. Althoughfacially complex, the process is straightforward in practice. See, e.g.,U.S. Pat. No. 6,187,287, incorporated fully herein by reference.

In addition to entire immunoglobulins (or their recombinantcounterparts), immunoglobulin fragments comprising the epitope bindingsite (e.g., Fab′, F(ab′)₂, or other fragments) may be synthesized.“Fragment,” or minimal immunoglobulins may be designed utilizingrecombinant immunoglobulin techniques. For instance “Fv” immunoglobulinsfor use in the present invention may be produced by synthesizing avariable light chain region and a variable heavy chain region.Combinations of antibodies are also of interest, e.g. diabodies, whichcomprise two distinct Fv specificities.

Immunoglobulins may be modified post-translationally, e.g. to addchemical linkers, detectable moieties, such as fluorescent dyes,enzymes, substrates, chemiluminescent moieties and the like, or specificbinding moieties, such as streptavidin, avidin, or biotin, and the likemay be utilized in the methods and compositions of the presentinvention.

Methods of Polypeptide Synthesis

Transformed mating competent haploid yeast cells provide a geneticmethod that enables subunit pairing of a desired protein. Haploid yeaststrains are transformed with each of two expression vectors, a firstvector to direct the synthesis of one polypeptide chain and a secondvector to direct the synthesis of a second, non-identical polypeptidechain. The two haploid strains are mated to provide a diploid host whereoptimized target protein production can be obtained.

Optionally, additional non-identical coding sequence(s) are provided.Such sequences may be present on additional expression vectors or in thefirst or the second expression vectors. As is known in the art, multiplecoding sequences may be independently expressed from individualpromoters; or may be coordinately expressed through the inclusion of an“internal ribosome entry site” or “IRES”, which is an element thatpromotes direct internal ribosome entry to the initiation codon, such asATG, of a cistron (a protein encoding region), thereby leading to thecap-independent translation of the gene. IRES elements functional inyeast are described by Thompson et al. (2001) P.N.A.S. 98:12866-12868.

In one embodiment of the invention, antibody sequences are produced incombination with a secretary J chain, which provides for enhancedstability of IgA (see U.S. Pat. Nos. 5,959,177; and 5,202,422).

The two haploid yeast strains are each auxotrophic, and requiresupplementation of media for growth of the haploid cells. The pair ofauxotrophs are complementary, such that the diploid product will grow inthe absence of the supplements required for the haploid cells. Many suchgenetic markers are known in yeast, including requirements for aminoacids (e.g. met, lys, his, arg, etc.), nucleosides (e.g. ura3, ade1,etc.); and the like. Amino acid markers may be preferred for the methodsof the invention.

The two transformed haploid cells may be genetically crossed and diploidstrains arising from this mating event selected by their hybridnutritional requirements. Alternatively, populations of the twotransformed haploid strains are spheroplasted and fused, and diploidprogeny regenerated and selected. By either method, diploid strains canbe identified and selectively grown because, unlike their haploidparents, they do not have the same nutritional requirements. Forexample, the diploid cells may be grown in minimal medium. The diploidsynthesis strategy has certain advantages. Diploid strains have thepotential to produce enhanced levels of heterologous protein throughbroader complementation to underlying mutations, which may impact theproduction and/or secretion of recombinant protein.

In one embodiment of the invention, each of the haploid strains istransformed with a library of polypeptides, e.g. a library of antibodyheavy or light chains. Transformed haploid cells that synthesize thepolypeptides are mated with the complementary haploid cells. Theresulting diploid cells are screened for functional protein. The diploidcells provide a means of rapidly, conveniently and inexpensivelybringing together a large number of combinations of polypeptides forfunctional testing. This technology is especially applicable for thegeneration of heterodimeric protein products, where optimized subunitsynthesis levels are critical for functional protein expression andsecretion.

In another embodiment of the invention, the expression level ratio ofthe two subunits is regulated in order to maximize product generation.Heterodimer subunit protein levels have been shown previously to impactthe final product generation (Simmons L C, J Immunol Methods. 2002 May1; 263(1-2):133-47). Regulation can be achieved prior to the mating stepby selection for a marker present on the expression vector. By stablyincreasing the copy number of the vector, the expression level can beincreased. In some cases, it may be desirable to increase the level ofone chain relative to the other, so as to reach a balanced proportionbetween the subunits of the polypeptide. Antibiotic resistance markersare useful for this purpose, e.g. Zeocin resistance marker, 6418resistance, etc. and provide a means of enrichment for strains thatcontain multiple integrated copies of an expression vector in a strainby selecting for transformants that are resistant to higher levels ofZeocin or G418. The proper ratio, e.g. 1:1; 1:2; etc. of the subunitgenes may be important for efficient protein production. Even when thesame promoter is used to transcribe both subunits, many other factorscontribute to the final level of protein expressed and therefore, it canbe useful to increase the number of copies of one encoded gene relativeto the other. Alternatively, diploid strains that produce higher levelsof a polypeptide, relative to single copy vector strains, are created bymating two haploid strains, both of which have multiple copies of theexpression vectors.

Host cells are transformed with the above-described expression vectors,mated to form diploid strains, and cultured in conventional nutrientmedia modified as appropriate for inducing promoters, selectingtransformants or amplifying the genes encoding the desired sequences. Anumber of minimal media suitable for the growth of yeast are known inthe art. Any of these media may be supplemented as necessary with salts(such as sodium chloride, calcium, magnesium, and phosphate), buffers(such as HEPES), nucleosides (such as adenosine and thymidine),antibiotics, trace elements, and glucose or an equivalent energy source.Any other necessary supplements may also be included at appropriateconcentrations that would be known to those skilled in the art. Theculture conditions, such as temperature, pH and the like, are thosepreviously used with the host cell selected for expression, and will beapparent to the ordinarily skilled artisan.

Secreted proteins are recovered from the culture medium. A proteaseinhibitor, such as phenyl methyl sulfonyl fluoride (PMSF) may be usefulto inhibit proteolytic degradation during purification, and antibioticsmay be included to prevent the growth of adventitious contaminants. Thecomposition may be concentrated, filtered, dialyzed, etc., using methodsknown in the art.

The diploid cells of the invention are grown for production purposes.Such production purposes desirably include growth in minimal media,which media lacks pre-formed amino acids and other complex biomolecules,e.g. media comprising ammonia as a nitrogen source, and glucose as anenergy and carbon source, and salts as a source of phosphate, calciumand the like. Preferably such production media lacks selective agentssuch as antibiotics, amino acids, purines, pyrimidines, etc. The diploidcells can be grown to high cell density, for example at least about 50g/L; more usually at least about 100 g/L; and may be at least about 300,about 400, about 500 g/L or more.

In one embodiment of the invention, the growth of the subject cells forproduction purposes is performed at low temperatures, which temperaturesmay be lowered during log phase, during stationary phase, or both. Theterm “low temperature” refers to temperatures of at least about 15° C.,more usually at least about 17° C., and may be about 20° C., and isusually not more than about 25° C., more usually not more than about 22°C. Growth temperature can impact the production of full-length secretedproteins in production cultures, and decreasing the culture growthtemperature can strongly enhances the intact product yield. Thedecreased temperature appears to assist intracellular traffickingthrough the folding and post-translational processing pathways used bythe host to generate the target product, along with reduction ofcellular protease degradation.

The methods of the invention provide for expression of secreted, activeprotein, particularly secreted, active antibodies, where “activeantibodies”, as used herein, refers to a correctly folded multimer of atleast two properly paired chains, which accurately binds to its cognateantigen. Expression levels of active protein are usually at least about50 mg/liter culture, more usually at least about 100 mg/liter,preferably at least about 500 mg/liter, and may be 1000 mg/liter ormore.

The methods of the invention can provide for increased stability of thehost and heterologous coding sequences during production. The stabilityis evidenced, for example, by maintenance of high levels of expressionof time, where the starting level of expression is decreased by not morethan about 20%, usually not more than 10%, and may be decreased by notmore than about 5% over about 20 doublings, 50 doublings, 100 doublings,or more.

The strain stability also provides for maintenance of heterologous genesequence integrity over time, where the sequence of the active codingsequence and requisite transcriptional regulatory elements aremaintained in at least about 99% of the diploid cells, usually in atleast about 99.9% of the diploid cells, and preferably in at least about99.99% of the diploid cells over about 20 doublings, 50 doublings, 100doublings, or more. Preferably, substantially all of the diploid cellsmaintain the sequence of the active coding sequence and requisitetranscriptional regulatory elements.

It is to be understood that this invention is not limited to theparticular methodology, protocols, cell lines, animal species or genera,constructs, and reagents described, as such may, of course, vary. It isalso to be understood that the terminology used herein is for thepurpose of describing particular embodiments only, and is not intendedto limit the scope of the present invention, which will be limited onlyby the appended claims.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood to one of ordinary skill inthe art to which this invention belongs. Although any methods, devicesand materials similar or equivalent to those described herein can beused in the practice or testing of the invention, the preferred methods,devices and materials are now described.

All publications mentioned herein are incorporated herein by referencefor the purpose of describing and disclosing, for example, the celllines, constructs, and methodologies that are described in thepublications, which might be used in connection with the presentlydescribed invention. The publications discussed above and throughout thetext are provided solely for their disclosure prior to the filing dateof the present application. Nothing herein is to be construed as anadmission that the inventors are not entitled to antedate suchdisclosure by virtue of prior invention.

The following examples are put forth so as to provide those of ordinaryskill in the art with a complete disclosure and description of how tomake and use the subject invention, and are not intended to limit thescope of what is regarded as the invention. Efforts have been made toensure accuracy with respect to the numbers used (e.g. amounts,temperature, concentrations, etc.) but some experimental errors anddeviations should be allowed for. Unless otherwise indicated, parts areparts by weight, molecular weight is average molecular weight,temperature is in degrees centigrade; and pressure is at or nearatmospheric.

EXPERIMENTAL Example 1

To demonstrate the efficacy of the diploid antibody production methodthe following reagents were prepared.

Antibody Genes:

Genes were cloned and constructed that directed the synthesis of threeforms of a chimeric humanized mouse monoclonal antibody OKT3. Thesources of the variable regions for use in these constructs can be foundin Genbank. Accession number A22261; mouse OKT3 heavy chain(International Patent Application WO 9109967-A 3 11 Jul. 1991).Accession number A22259; mouse OKT3 light chain (International PatentApplication WO 9109967-A 3 11 Jul. 1991).

All three forms utilized the identical V_(κ)C_(κ) light chain gene (SEQID NO: 10). For the three heavy chain genes, all encoded the identicalmouse variable region (V_(h)) but differed from each other in the aminoacid sequence of the human heavy chain constant regions. The firstconstruct directed the synthesis of a full-length wild-type heavy chain(C_(γt)) with its single normal N-linked glycosylation site present(full-length glycosylated heavy chain) (SEQ ID NO: 13 and No 14). Thesecond gene directed the synthesis of a non-glycosylated heavy chaincreated by mutating a nucleotide in the sequence so that a threonine atposition 301 was changed to an alanine in the glycosylation siterecognition sequence (ASN-X-Thr/Ser) (full-length non-glycosylated heavychain) (SEQ ID NO: 15). The third gene construct directed the synthesisof a heavy chain in which most of the constant region was deleted afterthe hinge region (Fab heavy chain) (SEQ ID NO: 16).

Expression Vector:

The vector contains the following functional components: 1) a mutantColE1 origin of replication, which facilitates the replication of theplasmid vector in cells of the bacterium Escherichia coli; 2) abacterial Sh ble gene, which confers resistance to the antibiotic Zeocinand serves as the selectable marker for transformations of both E. coliand P. pastoris; 3) an expression cassette composed of theglyceraldehyde dehydrogenase gene (GAP gene) promoter, fused tosequences encoding the Saccharomyces cerevisiae alpha mating factor prepro secretion leader sequence, followed by sequences encoding a P.pastoris transcriptional termination signal from the P. pastoris alcoholoxidase I gene (AOX1). The Zeocin resistance marker gene provides ameans of enrichment for strains that contain multiple integrated copiesof an expression vector in a strain by selecting for transformants thatare resistant to higher levels of Zeocin.

P. pastoris strains: The auxotrophic strains used for this example arethe P. pastoris ade1 and ura3 strains, which require supplementationwith adenine and uracil, respectively, for growth. Strains met1 and lys3have also been used. Although any two complementing sets of auxotrophicstrains could be used for the construction and maintenance of diploidstrains, these two strains are especially suited for this method for tworeasons. First, they grow more slowly than diploid strains that are theresult of their mating or fusion. Thus, if a small number of haploidade1 or ura3 cells remain present in a culture or arise through meiosisor other mechanism, the diploid strain should outgrow them in culture.

The second is that it is easy to monitor the sexual state of thesestrains since colonies of the diploid product of their mating are anormal white or cream color, whereas cells of any strains that arehaploid ade1 mutants in a culture form a colony with distinct pink incolor. In addition, any strains that are haploid ura3 mutants areresistant to the drug 5-fluoro-orotic acid (FOA) and can be sensitivelyidentified by plating samples of a culture on minimal medium+uracilplates with FOA. On these plates, only uracil-requiring ura3 mutant(presumably haploid) strains can grow and form colonies. Thus, withhaploid parent strains marked with ade1 and ura3, one can readilymonitor the sexual state of the resulting antibody-producing diploidstrains (haploid versus diploid).

Methods

Construction of pGAPZ-Alpha Expression Vectors for Transcription ofLight and Heavy Chain Antibody Genes.

For cloning of both the light and heavy chain variable regions, cells ofa mouse OKT3 CD3 hybridoma cell line were grown and total RNA extracted.Two RT-PCR reactions were then performed, one specific to light and onespecific to heavy chain variable region encoding sequences of the OKT3antibody genes. The primers employed to amplify out the heavy and lightchain variable region were (SEQ ID NO:1)5′-CCGCTCGAGAAAAGAGAGGCTGAAGCTCAGGTCCAGCTGCAGCAGTC-3′ and (SEQ ID NO: 3)5′-CCGCTCGAGAAAAGAGAGGCTGAAGCTCAAATTGTTCTCACCCAGTCTCC-3′ along with (SEQID NO:2) 5′-TGGGCCCTTGGTGGAGGCTGAGGAGACTGTGAGAGTGGTGC-3′ and (SEQ IDNO:4) 5′-GACAGATGGTGCAGCCACAGCCCGGTTTATTTCCAACTTTGTCC-3′ for therespective variable regions.

For the human heavy and light chain constant region genes, a humanleukocyte 5′-stretch plus cDNA library was purchased from Clontech (HL5019t). Two PCR reactions were performed on this library using primersspecific for the heavy and light chain constant regions, respectively(Heavy chain: (SEQ ID NO:6)5′-GCACCACTCTCACAGTCTCCTCAGCCTCCACCAAGGGCCCA-3 and (SEQ ID NO:5)5′-ATAAGAATGCGGCCGCTCATTTACCCGGAGACAGGGAG-3′ for full length along with(SEQ ID NO:7) 5′-TGCGGCCGCTCATGGGCACGGTGGGCATGTGT-3′ for FABgeneration′; Light chain: (SEQ ID NO:9)5′-GGACAAAGTTGGAAATAAACCGGGCTGTGGCTGCACCATCTGTC-3′ and (SEQ ID NO:8)5′-ATAAGAATGCGGCCGCTAACACTCTCCCCTGTTGAAGCT-3′.

A DNA sequence encoding the mouse light chain variable region was fusedin frame to a sequence encoding the human light chain constant region(SEQ ID NO: 11 and SEQ ID NO:12). A fragment encoding the final fusionconstruct was inserted into P. pastoris expression vector pGAPZ-alphavia ligation through 5′-XhoI and 3′-NotI sites in pGAPZ-alpha. DNAsequence encoding the mouse heavy variable region was fused in frame tosequences encoding each of the three human heavy chain constant regions.These fusion products were then inserted using a similar 5′-XhoI and3′-NotI strategy into pGAPZ-alpha. (SEQ ID NO:13 and SEQ ID NO: 14 forthe glycosylated version; SEQ ID NO: 15 for the aglycosylated version;SEQ ID NO: 16 for the Fab fragment). The proper antibody gene DNAsequences in all vectors were confirmed by direct DNA sequencing priorto further work.

Transformation of Expression Vectors into Haploid Adel Ura3, Met1 andLys3 Host Strains of P. pastoris.

All methods used for transformation of haploid P. pastoris strains andgenetic manipulation of the P. pastoris sexual cycle were as describedin Higgins, D. R., and Cregg, J. M., Eds. 1998. Pichia Protocols.Methods in Molecular Biology. Humana Press, Totowa, N.J.

Prior to transformation, each expression vector was linearized withinthe GAP promoter sequences with AvrII to direct the integration of thevectors into the GAP promoter locus of the P. pastoris genome. Samplesof each vector were then individually transformed into electrocompetentcultures of the ade1, ura3, met1 and lys3 strains by electroporation andsuccessful transformants were selected on YPD Zeocin plates by theirresistance to this antibiotic. Resulting colonies were selected,streaked for single colonies on YPD Zeocin plates and then examined forthe presence of the antibody gene insert by a PCR assay on genomic DNAextracted from each strain for the proper antibody gene insert and/or bythe ability of each strain to synthesize an antibody chain by a colonylift/immunoblot method (Wung et. al. Biotechniques 21 808-812 (1996).Haploid ade1, met1 and lys3 strains expressing one of the three heavychain constructs were collected for diploid constructions along withhaploid ura3 strain expressing light chain gene. The haploid expressingheavy chain genes were mated with the appropriate light chain haploidura3 to generate diploid secreting protein.

Mating of Haploid Strains Synthesizing a Single Antibody Chain andSelection of Diploid Derivatives Synthesizing Tetrameric FunctionalAntibodies.

To mate P. pastoris haploid strains, each ade1 (or met1 or lys3) heavychain producing strain to be crossed was streaked across a rich YPDplate and the ura3 light chain producing strain was streaked across asecond YPD plate (˜10 streaks per plate). After one or two daysincubation at 30° C., cells from one plate containing heavy chainstrains and one plate containing ura3 light chain strains weretransferred to a sterile velvet cloth on a replica-plating block in across hatched pattern so that each heavy chain strain contained a patchof cells mixed with each light chain strain. The cross-streaked replicaplated cells were then transferred to a mating plate and incubated at25° C. to stimulate the initiation of mating between strains. After twodays, the cells on the mating plates were transferred again to a sterilevelvet on a replica-plating block and then transferred to minimal mediumplates. These plates were incubated at 30° C. for three days to allowfor the selective growth of colonies of prototrophic diploid strains.Colonies that arose were picked and streaked onto a second minimalmedium plate to single colony isolate and purify each diploid strain.The resulting diploid cell lines were then examined for antibodyproduction.

Putative diploid strains were tested to demonstrate that they werediploid and contained both expression vectors for antibody production.For diploidy, samples of a strain were spread on mating plates tostimulate them to go through meiosis and form spores. Haploid sporeproducts were collected and tested for phenotype. If a significantpercentage of the resulting spore products were single or doubleauxotrophs we concluded that the original strain must have been diploid.Diploid strains were examined for the presence of both antibody genes byextracting genomic DNA from each and utilizing this DNA in PCR reactionsspecific for each gene.

Fusion of Haploid Strains Synthesizing a Single Antibody Chain andSelection of Diploid Derivatives Synthesizing Tetrameric FunctionalAntibodies.

As an alternative to the mating procedure described above, individualcultures of single-chain antibody producing haploid ade1 and ura3strains were spheroplasted and their resulting spheroplasts fused usingpolyethelyne glycol/CaCl₂. The fused haploid strains were then embeddedin agar containing 1 M sorbitol and minimal medium to allow diploidstrains to regenerate their cell wall and grow into visible colonies.Resulting colonies were picked from the agar, streaked onto a minimalmedium plate, and the plates incubated for two days at 30° C. togenerate colonies from single cells of diploid cell lines. The resultingputative diploid cell lines were then examined for diploidy and antibodyproduction as described above.

Purification and Analysis of Antibodies.

A diploid strain for the production of full length antibody was derivedthrough the mating of ura3 light chain strain 2252 and lys3 heavy chainstrain 2254 using the methods described above. Culture media fromshake-flask or fermenter cultures of diploid P. pastoris expressionstrains were collected and examined for the presence of antibody proteinvia SDS-PAGE and immunoblotting using antibodies directed against heavyand light chains of human IgG, or specifically against the heavy chainof IgG. The data is shown in FIG. 2.

To purify the yeast secreted antibodies, clarified media from antibodyproducing cultures were passed through a protein A column and afterwashing with 20 mM sodium phosphate, pH 7.0, binding buffer, protein Abound protein was eluted using 0.1 M glycine HCl buffer, pH 3.0.Fractions containing the most total protein were examined by Coomasieblue strained SDS-PAGE and immunoblotting for antibody protein.Fractions were also examined via an ELISA assay in which microtiterplates were first coated with F(ab′)2 goat anti-human IgG, Fcγ (JacksonImmuno, Cat No. 109-006-008). Next plates were reacted with selecteddilutions of yeast made antibodies. Finally, plates were reacted withHRP-conjugated goat anti-human F(ab′)2 fragment of IgG F(ab′)2 (JacksonImmuno, Cat No. 109-036-097). Plates were then developed with TMPsubstrate (Sigma Chemical) and reactions were quenched with 0.5 M HCl.Results were quantitated on a BioRad microtiter plate reader at 415 nm.The data is illustrated in FIG. 3.

Assay for Antibody Activity.

The recombinant yeast-derived chimeric antibody was evaluated forfunctional activity through immunohistochemical staining of cellscontaining the target antigen. The chimeric antibody selectivelyrecognizes the CD3 complex found on T cells. Jurkat T cells wereemployed as a source of antigen and cell surface staining was conductedusing procedures described in Andersson and Sander (Immunol Lett. 1989Jan. 31; 20(2):115-20) or Andersson et. al. (Eur J Immunol. 1988December; 18(12):2081-4).

Jurkat T cells were immobilized on glass slides, blocked with theappropriate blocking serum and stained with mammalian and yeastgenerated recombinant primary antibody for 1 hour. The immobilizedsamples were then treated with peroxidase blocking agent followed bystaining with a biotinylated Fc selective secondary antibody that isspecific for each form of the antibody (anti-mouse for the mammalian andanti-human for the yeast). Detection was performed using aHRP-Streptavidin system. Digital imaging was performed to collect thedata for each stained sample. Positive signal is detected in samples viaa dark staining of the cells observed in the panels formammalian-derived and yeast-derived OKT-3. This is data is shown in FIG.4.

What is claimed is:
 1. A method for the synthesis of a secretedheteromultimeric protein comprising at least two non-identical subunitpolypeptide chains in a Pichia pastoris diploid cell, the methodcomprising: (a) transforming a first auxotrophic Pichia pastoris haploidcell with a linearized first expression vector, said expression vectorcomprising a nucleic acid sequence encoding a first subunit of saidheteromultimeric protein, operably linked to a first Pichia pastorispromoter whereby the first expression vector comprising a nucleic acidsequence encoding the first subunit of said protein becomes integratedinto the gene locus comprising said Pichia pastoris promoter; (b)transforming a second auxotrophic Pichia pastoris haploid cell with alinearized second expression vector, said expression vector comprising anucleic acid sequence encoding a second subunit of said heteromultimericprotein, operably linked to a second Pichia pastoris promoter wherebythe second expression vector comprising said nucleic acid sequenceencoding said second subunit of said heteromultimeric protein becomesintegrated into the gene locus comprising said second Pichia pastorispromoter; (c) generating a putative diploid Pichia pastoris cell bymating or fusion of said first and second Pichia pastoris haploid cells;(d) determining whether the putative diploid cell is diploid by (i)permitting said putative diploid cell to go through meiosis and formspores; (ii) determining if a significant percentage of the resultingspore products are single or double auxotrophs and (iii) based thereondetermining that the putative diploid Pichia pastoris cell is diploid;and (e) culturing said diploid Pichia pastoris cell in a culture mediumunder conditions wherein said first and said second subunits areexpressed by said diploid Pichia pastoris cell and secreted as saidheteromultimeric protein; and (f) isolating the secretedheteromultimeric protein from the culture medium.
 2. The methodaccording to claim 1, wherein said heteromultimeric protein is anantibody comprising at least a variable region of a heavy and a lightchain.
 3. The method according to claim 2, wherein said heteromultimericprotein is an antibody comprising at least a variable and a constantregion of a heavy and a light chain.
 4. The method according to claim 2,wherein said first expression vector comprises a nucleic acid sequenceencoding a library of light or heavy chain sequences and said secondexpression vector comprises a nucleic acid sequence encoding a singlelight or heavy chain sequence.
 5. The method according to claim 2,wherein said first expression vector comprises a nucleic acid sequenceencoding a library of light or heavy chain sequences and said secondexpression vector comprises a nucleic acid sequence encoding a libraryof light or heavy chain sequences.
 6. The method according to claim 1,wherein said first and said second Pichia pastoris haploid cells arecomplementary auxotrophs.
 7. The method according to claim 6, whereinsaid step of generating a diploid cell from said first and second Pichiapastoris haploid cells comprises mating said haploid Pichia pastoriscells.
 8. The method according to claim 6, wherein said step ofgenerating a diploid cell from said first and second Pichia pastorishaploid cells comprises spheroplast fusion of said first and secondhaploid Pichia pastoris cells.
 9. The method according to claim 1,further comprising the step of calibrating the level of expression ofsaid first or said second subunit prior to generating said diploid cell.10. The method according to claim 1, wherein said first Pichia pastorispromoter and said second Pichia pastoris promoter are the same.
 11. Themethod according to claim 1, wherein said first Pichia pastoris promoterand said second Pichia pastoris promoter are different.
 12. The methodaccording to claim 1, wherein one or both of said Pichia pastorispromoters are constitutive promoters.
 13. The method according to claim1, wherein one or both of said Pichia pastoris promoters are induciblepromoters.
 14. The method according to claim 1, wherein said firstand/or second Pichia pastoris promoter is a glyceraldehyde-3-phosphatedehydrogenase (GAP) promoter.
 15. The method according to claim 1,wherein said non-identical subunit polypeptide chains comprises anoptimized signal sequence for diploid secretion and expression.
 16. Themethod according to claim 1, wherein said culturing step is performed inminimal media.
 17. The method according to claim 16, wherein saidminimal media lacks selective agents.
 18. The method according to claim1, wherein said culturing step is performed at a low temperature. 19.The method according to claim 1, wherein said first and/or secondauxotrophic Pichia pastoris haploid cells comprise ade1, ura3, met1 orlys3 auxotrophic strains.
 20. The method according to claim 1, whereinthe presence of the genes encoding the heteromultimeric protein in thediploid Pichia pastoris cell is confirmed by a PCR assay and/or bydetecting the ability of the diploid cell to synthesize saidheteromultimeric protein.
 21. The method according to claim 20, whereinsaid heteromultimeric protein is an antibody or antigen binding fragmentthereof.
 22. A culture comprising diploidal Pichia pastoris cellsproduced according to claim 1, which express and secrete theheteromultimeric protein.
 23. The culture of claim 22, wherein theheteromultimeric protein is an antibody.